The head of an Islamic charity was arrested yesterday and charged with dumping documents related to a Midtown high-rise whose rent payments allegedly helped fund Iran’s nuclear program.

FBI agents tailed Farshid Jahedi Thursday after a grand jury subpoenaed him for records dealing with 650 Fifth Ave., a 36-story office tower that houses the Juicy Couture flagship store, according to a complaint filed in Manhattan federal court.

After getting off a commuter train, Jahedi allegedly drove to a public trash can and tossed in torn papers that tied the building to Assa Corp., which the feds claim is a front for Iran’s state-owned Bank Melli.

Jahedi, president of the Alavi Foundation, had promised not to destroy any records, the complaint says.

The foundation was founded by Reza Shah Pahlavi, but his family lost control of it after the shah’s ouster in 1979.